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Hu Z, Lin G, Zhang M, Piao S, Fan J, Liu J, Liu P, Fu S, Sun W, Li L, Qiu X, Zhang J, Yang Y, Zhou C. Mechanistic Characterization of De Novo Generation of Variable Number Tandem Repeats in Circular Plasmids during Site-Directed Mutagenesis and Optimization for Coding Gene Application. Adv Biol (Weinh) 2024:e2400084. [PMID: 38880850 DOI: 10.1002/adbi.202400084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/21/2024] [Indexed: 06/18/2024]
Abstract
Site-directed mutagenesis for creating point mutations, sometimes, gives rise to plasmids carrying variable number tandem repeats (VNTRs) locally, which are arbitrarily regarded as polymerase chain reaction (PCR) related artifacts. Here, the alternative end-joining mechanism is reported rather than PCR artifacts accounts largely for that VNTRs formation and expansion. During generating a point mutation on GPLD1 gene, an unexpected formation of VNTRs employing the 31 bp mutagenesis primers is observed as the repeat unit in the pcDNA3.1-GPLD1 plasmid. The 31 bp VNTRs are formed in 24.75% of the resulting clones with copy number varied from 2 to 13. All repeat units are aligned with the same orientation as GPLD1 gene. 43.54% of the repeat junctions harbor nucleotide mutations while the rest don't. Their demonstrated short primers spanning the 3' part of the mutagenesis primers are essential for initial creation of the 2-copy tandem repeats (TRs) in circular plasmids. The dimerization of mutagenesis primers by the alternative end-joining in a correct orientation is required for further expansion of the 2-copy TRs. Lastly, a half-double priming strategy is established, verified the findings and offered a simple method for VNTRs creation on coding genes in circular plasmids without junction mutations.
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Affiliation(s)
- Ziqi Hu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Guochao Lin
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Mingzhu Zhang
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Shengwen Piao
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jiankun Fan
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jichao Liu
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Peng Liu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Songbin Fu
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, China
| | - Wenjing Sun
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, China
| | - Li Li
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Xiaohong Qiu
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Jinwei Zhang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Yu Yang
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Chunshui Zhou
- The Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- The Second Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
- Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Harbin Medical University, Ministry of Education, China
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Fages V, Bourre F, Larrue R, Wenzel A, Gibier JB, Bonte F, Dhaenens CM, Kidd K, Kmoch S, Bleyer A, Glowacki F, Grunewald O. Description of a New Simple and Cost-Effective Molecular Testing That Could Simplify MUC1 Variant Detection. Kidney Int Rep 2024; 9:1451-1457. [PMID: 38707821 PMCID: PMC11068942 DOI: 10.1016/j.ekir.2024.01.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/23/2024] [Accepted: 01/29/2024] [Indexed: 05/07/2024] Open
Abstract
Introduction Patients with autosomal dominant tubulointerstitial kidney disease (ADTKD) usually present with nonspecific progressive chronic kidney disease (CKD) with mild to negative proteinuria and a family history. ADTKD-MUC1 leads to the formation of a frameshift protein that accumulates in the cytoplasm, leading to tubulointerstitial damage. ADTKD-MUC1 prevalence remains unclear because MUC1 variants are not routinely detected by standard next-generation sequencing (NGS) techniques. Methods We developed a bioinformatic counting script that can detect specific genetic sequences and count the number of occurrences. We used DNA samples from 27 patients for validation, 11 of them were patients from the Lille University Hospital in France and 16 were from the Wake Forest Hospital, NC. All patients from Lille were tested with an NGS gene panel with our script and all patients from Wake Forest Hospital were tested with the snapshot reference technique. Between January 2018 and February 2023, we collected data on all patients diagnosed with MUC1 variants with this script. Results A total of 27 samples were tested anonymously by the BROAD Institute reference technique for confirmation and we were able to get a 100% concordance for MUC1 diagnosis. Clinico-biologic characteristics in our cohort were similar to those previously described in ADTKD-MUC1. Conclusion We describe a new simple and cost-effective method for molecular testing of ADTKD-MUC1. Genetic analyses in our cohort suggest that MUC1 might be the first cause of ADTKD. Increasing the availability of MUC1 diagnosis tools will contribute to a better understanding of the disease and to the development of specific treatments.
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Affiliation(s)
- Victor Fages
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Florentin Bourre
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Romain Larrue
- Service de Toxicologie et Génopathies, CHU Lille, Lille, France
| | - Andrea Wenzel
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Cologne, Germany
| | | | - Fabrice Bonte
- Functional and Structural Platform, Université de Lille, Lille, France
| | - Claire-Marie Dhaenens
- Department of Biochemistry and Molecular Biology, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire de Lille, Lille, France
| | - Kendrah Kidd
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Stanislav Kmoch
- First Faculty of Medicine, Charles University, Nové Město, Czechia
| | - Anthony Bleyer
- Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - François Glowacki
- Nephrology, Centre Hospitalier Regional Universitaire de Lille, Lille, France
| | - Olivier Grunewald
- Neuroscience and Cognition, University Lille, Inserm, CHU Lille, Lille, France
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Jeong MS, Mun JY, Yang GE, Kim MH, Lee SY, Choi YH, Kim HS, Nam JK, Kim TN, Leem SH. Exploring the Relationship between CLPTM1L-MS2 Variants and Susceptibility to Bladder Cancer. Genes (Basel) 2023; 15:50. [PMID: 38254939 PMCID: PMC10815179 DOI: 10.3390/genes15010050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
CLPTM1L (Cleft Lip and Palate Transmembrane Protein 1-Like) has previously been implicated in tumorigenesis and drug resistance in cancer. However, the genetic link between CLPTM1L and bladder cancer remains uncertain. In this study, we investigated the genetic association of variable number of tandem repeats (VNTR; minisatellites, MS) regions within CLPTM1L with bladder cancer. We identified four CLPTM1L-MS regions (MS1~MS4) located in intron regions. To evaluate the VNTR polymorphic alleles, we analyzed 441 cancer-free controls and 181 bladder cancer patients. Our analysis revealed a higher frequency of specific repeat sizes within the MS2 region in bladder cancer cases compared to controls. Notably, 25 and 27 repeats were exclusively present in the bladder cancer group. Moreover, rare alleles within the medium-length repeat range (25-29 repeats) were associated with an elevated bladder cancer risk (odds ratio [OR] = 5.78, 95% confidence interval [CI]: 1.49-22.47, p = 0.004). We confirmed that all MS regions followed Mendelian inheritance, and demonstrated that MS2 alleles increased CLPTM1L promoter activity in the UM-UC3 bladder cancer cells through a luciferase assay. Our findings propose the utility of CLPTM1L-MS regions as DNA typing markers, particularly highlighting the potential of middle-length rare alleles within CLPTM1L-MS2 as predictive markers for bladder cancer risk.
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Affiliation(s)
- Mi-So Jeong
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea; (M.-S.J.); (J.-Y.M.); (G.-E.Y.); (M.-H.K.)
- Research Center, Dongnam Institute of Radiological & Medical Sciences (DIRAMS), Busan 46033, Republic of Korea
| | - Jeong-Yeon Mun
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea; (M.-S.J.); (J.-Y.M.); (G.-E.Y.); (M.-H.K.)
| | - Gi-Eun Yang
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea; (M.-S.J.); (J.-Y.M.); (G.-E.Y.); (M.-H.K.)
- Department of Health Sciences, The Graduated of Dong-A University, Busan 49315, Republic of Korea
| | - Min-Hye Kim
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea; (M.-S.J.); (J.-Y.M.); (G.-E.Y.); (M.-H.K.)
| | - Sang-Yeop Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang 28119, Republic of Korea;
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Anti-Aging Research Center, Dong-eui University, Busan 47227, Republic of Korea;
| | - Heui Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea;
| | - Jong-Kil Nam
- Department of Urology, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Research Institute for Convergence of Biomedical Science and Technology, Yangsan 50612, Republic of Korea;
| | - Tae Nam Kim
- Department of Urology, Pusan National University Hospital, Pusan National University School of Medicine, Biomedical Research Institute and Pusan National University Hospital, Busan 49241, Republic of Korea
| | - Sun-Hee Leem
- Department of Biomedical Sciences, Dong-A University, Busan 49315, Republic of Korea; (M.-S.J.); (J.-Y.M.); (G.-E.Y.); (M.-H.K.)
- Department of Health Sciences, The Graduated of Dong-A University, Busan 49315, Republic of Korea
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Klashami ZN, Mostafavi A, Roudbordeh MG, Abbasi A, Ebrahimi P, Asadi M, Amoli MM. Investigating the relationship between the VNTR variant of the interleukin-1 receptor antagonist gene and coronary in-stent restenosis. Mol Biol Rep 2023; 50:8575-8587. [PMID: 37644369 DOI: 10.1007/s11033-023-08759-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 08/31/2023]
Abstract
OBJECTIVE This study aimed to examine the association between the interleukin-1 receptor antagonist gene (IL-1RN) and coronary in-stent restenosis (ISR) through the analysis of the VNTR variant based on the previously reported results. MATERIALS AND METHODS The samples were classified into two clearly defined groups: the case group, which comprised 45 patients diagnosed with in-stent restenosis (ISR+), and the control group, which included 60 patients without ISR (ISR-). Polymerase chain reaction (PCR) was performed to examine the 86-bp VNTR variant of the IL-1RN gene. RESULTS In the analysis of six identified groups consisting of variant alleles of 86 base pairs of VNTR of the IL-1RN gene statistically significant difference was observed for the presence of IL1RN*2 allele between cases and controls (p = 0.04, OR; 0.045). CONCLUSION Individuals with allele 2 of the IL-1Ra gene may be more predisposed to ISR. This could be due to an imbalance between IL-1Ra and IL-1β which is crucial in preventing the initiation or advancement of inflammatory diseases in specific organs. The observed phenomenon can be characterized by increased production of IL-1β and potential reduction of IL-1Ra as a result of functional VNTR variation in IL-RN gene.
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Affiliation(s)
- Zeynab Nickhah Klashami
- Metabolic Disorders Research Centre, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Atoosa Mostafavi
- Department of Cardiology, Faculty of Medicine, Tehran university of medical sciences, Tehran, Iran
| | | | - Ali Abbasi
- Department of Cardiology, Faculty of Medicine, Tehran university of medical sciences, Tehran, Iran
| | - Pirooz Ebrahimi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata, Italy
| | - Mojgan Asadi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Centre, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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Ding YC, Adamson AW, Bakhtiari M, Patrick C, Park J, Laitman Y, Weitzel JN, Bafna V, Friedman E, Neuhausen SL. Variable number tandem repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG. Eur J Hum Genet 2023; 31:216-222. [PMID: 36434258 PMCID: PMC9905572 DOI: 10.1038/s41431-022-01238-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/10/2022] [Accepted: 11/08/2022] [Indexed: 11/27/2022] Open
Abstract
Despite substantial efforts in identifying both rare and common variants affecting disease risk, in the majority of diseases, a large proportion of unexplained genetic risk remains. We propose that variable number tandem repeats (VNTRs) may explain a proportion of the missing genetic risk. Herein, in a pilot study with a retrospective cohort design, we tested whether VNTRs are causal modifiers of breast cancer risk in 347 female carriers of the BRCA1 185delAG pathogenic variant, an important group given their high risk of developing breast cancer. We performed targeted-capture to sequence VNTRs, called genotypes with adVNTR, tested the association of VNTRs and breast cancer risk using Cox regression models, and estimated the effect size using a retrospective likelihood approach. Of 303 VNTRs that passed quality control checks, 4 VNTRs were significantly associated with risk to develop breast cancer at false discovery rate [FDR] < 0.05 and an additional 4 VNTRs had FDR < 0.25. After determining the specific risk alleles, there was a significantly earlier age at diagnosis of breast cancer in carriers of the risk alleles compared to those without the risk alleles for seven of eight VNTRs. One example is a VNTR in exon 2 of LINC01973 with a per-allele hazard ratio of 1.58 (1.07-2.33) and 5.28 (2.79-9.99) for the homozygous risk-allele genotype. Results from this first systematic study of VNTRs demonstrate that VNTRs may explain a proportion of the unexplained genetic risk for breast cancer.
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Affiliation(s)
- Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Aaron W Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Mehrdad Bakhtiari
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Carmina Patrick
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Jonghun Park
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Yael Laitman
- Oncogenetics Unit, Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel
| | - Jeffrey N Weitzel
- Latin American School of Oncology, Tuxla Gutierrez, Chiapas, MX and Natera, San Carlos, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Eitan Friedman
- Oncogenetics Unit, Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Center for Preventive Personalized Medicine, Assuta Medical Center, Tel Aviv, Israel
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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Park J, Bakhtiari M, Popp B, Wiesener M, Bafna V. Detecting tandem repeat variants in coding regions using code-adVNTR. iScience 2022; 25:104785. [PMID: 35982790 PMCID: PMC9379575 DOI: 10.1016/j.isci.2022.104785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/16/2022] [Accepted: 07/13/2022] [Indexed: 11/25/2022] Open
Abstract
The human genome contains more than one million tandem repeats (TRs), DNA sequences containing multiple approximate copies of a motif repeated contiguously. TRs account for significant genetic variation, with 50 + diseases attributed to changes in motif number. A few diseases have been to be caused by small indels in variable number tandem repeats (VNTRs) including poly-cystic kidney disease type 1 (MCKD1) and monogenic type 1 diabetes. However, small indels in VNTRs are largely unexplored mainly due to the long and complex structure of VNTRs with multiple motifs. We developed a method, code-adVNTR, that utilizes multi-motif hidden Markov models to detect both, motif count variation and small indels, within VNTRs. In simulated data, code-adVNTR outperformed GATK-HaplotypeCaller in calling small indels within large VNTRs. We used code-adVNTR to characterize coding VNTRs in the 1000 genomes data identifying many population-specific variants, and to reliably call MUC1 mutations for MCKD1. Detection of coding variants in tandem repeats is confounded by ambiguous mapping Our method, code-adVNTR, detects variants in coding VNTRs using multi-motif HMMs code-adVNTR outperforms GATK-HaplotypeCaller on indel detection in tandem repeats A known frameshift variant within a VNTR in MUC1 gene was accurately detected
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Affiliation(s)
- Jonghun Park
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mehrdad Bakhtiari
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Bernt Popp
- Institute of Human Genetics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Michael Wiesener
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
- Corresponding author
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7
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van Bree EJ, Guimarães RLFP, Lundberg M, Blujdea ER, Rosenkrantz JL, White FTG, Poppinga J, Ferrer-Raventós P, Schneider AFE, Clayton I, Haussler D, Reinders MJT, Holstege H, Ewing AD, Moses C, Jacobs FMJ. A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome Res 2022; 32:656-670. [PMID: 35332097 PMCID: PMC8997352 DOI: 10.1101/gr.275515.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable elements with gene-regulatory roles, which represents a major source of structural variability in the human population. We highlight the presence of structurally variable SVAs (SV-SVAs) in neurological disease-associated loci, and we further associate SV-SVAs to disease-associated SNPs and differential gene expression using luciferase assays and expression quantitative trait loci data. Finally, we genetically deleted SV-SVAs in the BIN1 and CD2AP Alzheimer's disease-associated risk loci and in the BCKDK Parkinson's disease-associated risk locus and assessed multiple aspects of their gene-regulatory influence in a human neuronal context. Together, this study reveals a novel layer of genetic variation in transposable elements that may contribute to identification of the structural variants that are the actual drivers of disease associations of GWAS loci.
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Affiliation(s)
- Elisabeth J van Bree
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Rita L F P Guimarães
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands
| | - Mischa Lundberg
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Elena R Blujdea
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Jimi L Rosenkrantz
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Fred T G White
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Josse Poppinga
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Paula Ferrer-Raventós
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Anne-Fleur E Schneider
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Isabella Clayton
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - David Haussler
- UC Santa Cruz Genomics Institute, and Howard Hughes Medical Institute, UC Santa Cruz, Santa Cruz, California 95064, USA
| | - Marcel J T Reinders
- Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands
| | - Henne Holstege
- Genomics of Neurodegenerative Diseases and Aging, Department of Human Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands.,Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Colette Moses
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank M J Jacobs
- Evolutionary Neurogenomics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands.,Amsterdam Neuroscience, Complex Trait Genetics, University of Amsterdam, Amsterdam, The Netherlands
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Yang JJ, Wang Z, Trucco EM, Buu A, Lin HC. Chronic pain and delinquency partially explain the effect of the DRD4 gene polymorphism on adult substance use. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2022; 48:235-244. [PMID: 34710332 DOI: 10.1080/00952990.2021.1977311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/31/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Background: The dopamine receptor D4 [DRD4] has been reported to be associated with substance use. Yet, the roles that health conditions and behaviors may play in such association are understudied.Objective: This longitudinal study investigated the potential mediation effects of chronic pain and delinquency in adolescence on the association between the DRD4 2-repeat allele and substance use in adulthood. Sex, witnessing violence, and experiencing violence were also examined as potential moderators for the mediation pathways.Methods: We used the restricted and candidate gene data from the National Longitudinal Study of Adolescent to Adult Health (Waves I-IV) to conduct secondary analysis (N = 8,671; 47% male). A two-step approach was adopted to examine the mediation effects regarding four substance use outcomes in adulthood: number of lifetime alcohol use disorder symptoms, lifetime regular smoker status, past-month smoking, and lifetime "pain killer" misuse. The moderation effects were investigated using stratification and permutation.Results: The DRD4 2-repeat allele was associated with all adulthood substance use outcomes through adolescent chronic pain and delinquency (AORs/IRR range 1.08-3.78; all ps<0.01). The association between delinquency and smoking was higher among females. The association between delinquency and substance use was lower among the participants who witnessed violence in adolescence.Conclusions: This study identified modifiable mediators underlying the association between the DRD4 2-repeat allele and substance use behaviors, concluding that chronic pain and delinquency partially explain the effect of the DRD4 gene polymorphism on adult substance use.
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Affiliation(s)
- James J Yang
- Department of Biostatistics and Data Science, School of Public Health, University of Texas, Houston, TX, USA
| | - Zhi Wang
- Department of Applied Health Science, School of Public Health, Indiana University, Bloomington, IN, USA
| | - Elisa M Trucco
- Department of Psychology, Florida International University, Miami, FL, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, USA
| | - Anne Buu
- Department of Health Promotion and Behavioral Sciences, School of Public Health, University of Texas, Houston, TX, USA
| | - Hsien-Chang Lin
- Department of Applied Health Science, School of Public Health, Indiana University, Bloomington, IN, USA
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Kasai S, Nishizawa D, Hasegawa J, Fukuda KI, Ichinohe T, Nagashima M, Hayashida M, Ikeda K. Short Tandem Repeat Variation in the CNR1 Gene Associated With Analgesic Requirements of Opioids in Postoperative Pain Management. Front Genet 2022; 13:815089. [PMID: 35360861 PMCID: PMC8963810 DOI: 10.3389/fgene.2022.815089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/02/2022] [Indexed: 11/25/2022] Open
Abstract
Short tandem repeats (STRs) and variable number of tandem repeats (VNTRs) that have been identified at approximately 0.7 and 0.5 million loci in the human genome, respectively, are highly multi-allelic variations rather than single-nucleotide polymorphisms. The number of repeats of more than a few thousand STRs was associated with the expression of nearby genes, indicating that STRs are influential genetic variations in human traits. Analgesics act on the central nervous system via their intrinsic receptors to produce analgesic effects. In the present study, we focused on STRs and VNTRs in the CNR1, GRIN2A, PENK, and PDYN genes and analyzed two peripheral pain sensation-related traits and seven analgesia-related traits in postoperative pain management. A total of 192 volunteers who underwent the peripheral pain sensation tests and 139 and 252 patients who underwent open abdominal and orthognathic cosmetic surgeries, respectively, were included in the study. None of the four STRs or VNTRs were associated with peripheral pain sensation. Short tandem repeats in the CNR1, GRIN2A, and PENK genes were associated with the frequency of fentanyl use, fentanyl dose, and visual analog scale pain scores 3 h after orthognathic cosmetic surgery (Spearman’s rank correlation coefficient ρ = 0.199, p = 0.002, ρ = 0.174, p = 0.006, and ρ = 0.135, p = 0.033, respectively), analgesic dose, including epidural analgesics after open abdominal surgery (ρ = −0.200, p = 0.018), and visual analog scale pain scores 24 h after orthognathic cosmetic surgery (ρ = 0.143, p = 0.023), respectively. The associations between STRs in the CNR1 gene and the frequency of fentanyl use and fentanyl dose after orthognathic cosmetic surgery were confirmed by Holm’s multiple-testing correction. These findings indicate that STRs in the CNR1 gene influence analgesia in the orofacial region.
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Affiliation(s)
- Shinya Kasai
- Addictive Substance Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Daisuke Nishizawa
- Addictive Substance Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Junko Hasegawa
- Addictive Substance Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Ken-ichi Fukuda
- Department of Oral Health Science, Tokyo Dental College, Tokyo, Japan
| | - Tatsuya Ichinohe
- Department of Dental Anesthesiology, Tokyo Dental College, Tokyo, Japan
| | - Makoto Nagashima
- Department of Surgery, Toho University Sakura Medical Center, Sakura, Japan
| | - Masakazu Hayashida
- Department of Anesthesiology and Pain Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Kazutaka Ikeda
- Addictive Substance Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- *Correspondence: Kazutaka Ikeda,
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10
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Xiao X, Zhang CY, Zhang Z, Hu Z, Li M, Li T. Revisiting tandem repeats in psychiatric disorders from perspectives of genetics, physiology, and brain evolution. Mol Psychiatry 2022; 27:466-475. [PMID: 34650204 DOI: 10.1038/s41380-021-01329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 01/28/2023]
Abstract
Genome-wide association studies (GWASs) have revealed substantial genetic components comprised of single nucleotide polymorphisms (SNPs) in the heritable risk of psychiatric disorders. However, genetic risk factors not covered by GWAS also play pivotal roles in these illnesses. Tandem repeats, which are likely functional but frequently overlooked by GWAS, may account for an important proportion in the "missing heritability" of psychiatric disorders. Despite difficulties in characterizing and quantifying tandem repeats in the genome, studies have been carried out in an attempt to describe impact of tandem repeats on gene regulation and human phenotypes. In this review, we have introduced recent research progress regarding the genomic distribution and regulatory mechanisms of tandem repeats. We have also summarized the current knowledge of the genetic architecture and biological underpinnings of psychiatric disorders brought by studies of tandem repeats. These findings suggest that tandem repeats, in candidate psychiatric risk genes or in different levels of linkage disequilibrium (LD) with psychiatric GWAS SNPs and haplotypes, may modulate biological phenotypes related to psychiatric disorders (e.g., cognitive function and brain physiology) through regulating alternative splicing, promoter activity, enhancer activity and so on. In addition, many tandem repeats undergo tight natural selection in the human lineage, and likely exert crucial roles in human brain evolution. Taken together, the putative roles of tandem repeats in the pathogenesis of psychiatric disorders is strongly implicated, and using examples from previous literatures, we wish to call for further attention to tandem repeats in the post-GWAS era of psychiatric disorders.
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Affiliation(s)
- Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yi Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Critical Care Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Eye Center of Xiangya Hospital and Hunan Key Laboratory of Ophthalmology, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, China.
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11
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Rajabi F, Jabalameli N, Rezaei N. The Concept of Immunogenetics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:1-17. [DOI: 10.1007/978-3-030-92616-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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A multicenter case-control study of the effect of e-nos VNTR polymorphism on upper gastrointestinal hemorrhage in NSAID users. Sci Rep 2021; 11:19923. [PMID: 34620931 PMCID: PMC8497469 DOI: 10.1038/s41598-021-99402-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023] Open
Abstract
Bleeding in non-steroidal anti-inflammatory drug (NSAID) users limited their prescription. This first multicenter full case–control study (325 cases and 744 controls), explored the association of e-NOS intron 4 variable number tandem repeat (VNTR) polymorphism with upper gastrointestinal hemorrhage (UGIH) in NSAID exposed and unexposed populations and assessed any interaction between this polymorphism and NSAIDs. NSAID users carrying e-NOS intron 4 wild type genotype or VNTR polymorphism have higher odds of UGIH than those unexposed to NSAIDs [Odds Ratio (OR): 6.62 (95% Confidence Interval (CI): 4.24, 10.36) and OR: 5.41 (95% CI 2.62, 11.51), respectively], with no effect modification from VNTR polymorphism-NSAIDs interaction [Relative Excess Risk due to Interaction (RERI): −1.35 (95% CI −5.73, 3.03); Synergism Index (S): 0.77 (95% CI 0.31, 1.94)]. Similar findings were obtained for aspirin exposure. Non-aspirin NSAID users who carry e-NOS intron 4 VNTR polymorphism have lower odds of UGIH [OR: 4.02 (95% CI 1.85, 8.75) than those users with wild type genotype [OR: 6.52 (95% CI 4.09, 10.38)]; though the interaction estimates are not statistically significant [RERI: −2.68 (95% CI −6.67, 1.31); S: 0.53 (95% CI 0.18, 1.55)]. This exploratory study suggests that the odds of UGIH in NSAID or aspirin users does not modify according to patient´s e-NOS intron 4 genotype.
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13
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Gravdal A, Xiao X, Cnop M, El Jellas K, Johansson S, Njølstad PR, Lowe ME, Johansson BB, Molven A, Fjeld K. The position of single-base deletions in the VNTR sequence of the carboxyl ester lipase (CEL) gene determines proteotoxicity. J Biol Chem 2021; 296:100661. [PMID: 33862081 PMCID: PMC8692231 DOI: 10.1016/j.jbc.2021.100661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/05/2021] [Accepted: 04/12/2021] [Indexed: 02/06/2023] Open
Abstract
Variable number of tandem repeat (VNTR) sequences in the genome can have functional consequences that contribute to human disease. This is the case for the CEL gene, which is specifically expressed in pancreatic acinar cells and encodes the digestive enzyme carboxyl ester lipase. Rare single-base deletions (DELs) within the first (DEL1) or fourth (DEL4) VNTR segment of CEL cause maturity-onset diabetes of the young, type 8 (MODY8), an inherited disorder characterized by exocrine pancreatic dysfunction and diabetes. Studies on the DEL1 variant have suggested that MODY8 is initiated by CEL protein misfolding and aggregation. However, it is unclear how the position of single-base deletions within the CEL VNTR affects pathogenic properties of the protein. Here, we investigated four naturally occurring CEL variants, arising from single-base deletions in different VNTR segments (DEL1, DEL4, DEL9, and DEL13). When the four variants were expressed in human embryonic kidney 293 cells, only DEL1 and DEL4 led to significantly reduced secretion, increased intracellular aggregation, and increased endoplasmic reticulum stress compared with normal CEL protein. The level of O-glycosylation was affected in all DEL variants. Moreover, all variants had enzymatic activity comparable with that of normal CEL. We conclude that the longest aberrant protein tails, resulting from single-base deletions in the proximal VNTR segments, have highest pathogenic potential, explaining why DEL1 and DEL4 but not DEL9 and DEL13 have been observed in patients with MODY8. These findings further support the view that CEL mutations cause pancreatic disease through protein misfolding and proteotoxicity, leading to endoplasmic reticulum stress and activation of the unfolded protein response.
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Affiliation(s)
- Anny Gravdal
- The Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Xunjun Xiao
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine, St Louis, Missouri, USA
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium; Division of Endocrinology, ULB Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Khadija El Jellas
- The Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Stefan Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Pål R Njølstad
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Pediatrics and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
| | - Mark E Lowe
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Washington University School of Medicine, St Louis, Missouri, USA
| | - Bente B Johansson
- Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Pediatrics and Adolescent Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anders Molven
- The Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway.
| | - Karianne Fjeld
- The Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, Bergen, Norway; Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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14
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Bakhtiari M, Park J, Ding YC, Shleizer-Burko S, Neuhausen SL, Halldórsson BV, Stefánsson K, Gymrek M, Bafna V. Variable number tandem repeats mediate the expression of proximal genes. Nat Commun 2021; 12:2075. [PMID: 33824302 PMCID: PMC8024321 DOI: 10.1038/s41467-021-22206-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/17/2021] [Indexed: 12/12/2022] Open
Abstract
Variable number tandem repeats (VNTRs) account for significant genetic variation in many organisms. In humans, VNTRs have been implicated in both Mendelian and complex disorders, but are largely ignored by genomic pipelines due to the complexity of genotyping and the computational expense. We describe adVNTR-NN, a method that uses shallow neural networks to genotype a VNTR in 18 seconds on 55X whole genome data, while maintaining high accuracy. We use adVNTR-NN to genotype 10,264 VNTRs in 652 GTEx individuals. Associating VNTR length with gene expression in 46 tissues, we identify 163 "eVNTRs". Of the 22 eVNTRs in blood where independent data is available, 21 (95%) are replicated in terms of significance and direction of association. 49% of the eVNTR loci show a strong and likely causal impact on the expression of genes and 80% have maximum effect size at least 0.3. The impacted genes are involved in diseases including Alzheimer's, obesity and familial cancers, highlighting the importance of VNTRs for understanding the genetic basis of complex diseases.
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Affiliation(s)
- Mehrdad Bakhtiari
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jonghun Park
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Yuan-Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | | | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | | | | | - Melissa Gymrek
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA, USA.
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15
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Bolat H, Ercan ES, Ünsel-Bolat G, Tahillioğlu A, Yazici KU, Bacanli A, Pariltay E, Aygüneş Jafari D, Kosova B, Özgül S, Rohde LA, Akin H. DRD4 genotyping may differentiate symptoms of attention-deficit/hyperactivity disorder and sluggish cognitive tempo. ACTA ACUST UNITED AC 2020; 42:630-637. [PMID: 32491038 PMCID: PMC7678899 DOI: 10.1590/1516-4446-2019-0630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 01/17/2020] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Studies to reduce the heterogeneity of attention-deficit/hyperactivity disorder (ADHD) have increased interest in the concept of sluggish cognitive tempo (SCT). The aim of this study was to investigate if the prevalence of two variable-number tandem repeats (VNTRs) located within the 3'-untranslated region of the DAT1 gene and in exon 3 of the dopamine D4 receptor (DRD4) gene differ among four groups (31 subjects with SCT but no ADHD, 146 individuals with ADHD but no SCT, 67 subjects with SCT + ADHD, and 92 healthy controls). METHODS We compared the sociodemographic profiles, neurocognitive domains, and prevalence of two VNTRs in SCT and ADHD subjects versus typically developing (TD) controls. RESULTS The SCT without ADHD group had a higher proportion of females and lower parental educational attainment. Subjects in this group performed worse on neuropsychological tests, except for psychomotor speed and commission errors, compared to controls. However, the ADHD without SCT group performed significantly worse on all neuropsychological domains than controls. We found that 4R homozygosity for the DRD4 gene was most prevalent in the ADHD without SCT group. The SCT without ADHD group had the highest 7R allele frequency, differing significantly from the ADHD without SCT group. CONCLUSION The 7R allele of DRD4 gene was found to be significantly more prevalent in SCT cases than in ADHD cases. No substantial neuropsychological differences were found between SCT and ADHD subjects.
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Affiliation(s)
- Hilmi Bolat
- Department of Medical Genetics, Balikesir Atatürk City Hospital, Balikesir, Turkey
| | - Eyüp S Ercan
- Department of Child and Adolescent Psychiatry, Ege University, Izmir, Turkey
| | - Gül Ünsel-Bolat
- Department of Child and Adolescent Psychiatry, Balikesir University Faculty of Medicine, Balikesir, Turkey
| | - Akin Tahillioğlu
- Department of Child and Adolescent Psychiatry, Ege University, Izmir, Turkey
| | - Kemal U Yazici
- Department of Child and Adolescent Psychiatry, Firat University, Izmir, Turkey
| | - Ali Bacanli
- Department of Child and Adolescent Psychiatry, Baskent University, Izmir, Turkey
| | - Erhan Pariltay
- Department of Medical Genetics, Ege University, Izmir, Turkey
| | | | - Buket Kosova
- Department of Medical Biology, Ege University, Izmir, Turkey
| | - Semiha Özgül
- Department of Bioistatistics and Medical Informatics, Ege University, Izmir, Turkey
| | - Luis A Rohde
- Programa de Transtornos de Déficit de Atenção/Hiperatividade (ProDAH), Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Instituto Nacional de Psiquiatria do Desenvolvimento para Crianças e Adolescentes, São Paulo, SP, Brazil
| | - Haluk Akin
- Department of Medical Genetics, Ege University, Izmir, Turkey
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16
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Linthorst J, Meert W, Hestand MS, Korlach J, Vermeesch JR, Reinders MJT, Holstege H. Extreme enrichment of VNTR-associated polymorphicity in human subtelomeres: genes with most VNTRs are predominantly expressed in the brain. Transl Psychiatry 2020; 10:369. [PMID: 33139705 PMCID: PMC7608644 DOI: 10.1038/s41398-020-01060-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/27/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The human genome harbors numerous structural variants (SVs) which, due to their repetitive nature, are currently underexplored in short-read whole-genome sequencing approaches. Using single-molecule, real-time (SMRT) long-read sequencing technology in combination with FALCON-Unzip, we generated a de novo assembly of the diploid genome of a 115-year-old Dutch cognitively healthy woman. We combined this assembly with two previously published haploid assemblies (CHM1 and CHM13) and the GRCh38 reference genome to create a compendium of SVs that occur across five independent human haplotypes using the graph-based multi-genome aligner REVEAL. Across these five haplotypes, we detected 31,680 euchromatic SVs (>50 bp). Of these, ~62% were comprised of repetitive sequences with 'variable number tandem repeats' (VNTRs), ~10% were mobile elements (Alu, L1, and SVA), while the remaining variants were inversions and indels. We observed that VNTRs with GC-content >60% and repeat patterns longer than 15 bp were 21-fold enriched in the subtelomeric regions (within 5 Mb of the ends of chromosome arms). VNTR lengths can expand to exceed a critical length which is associated with impaired gene transcription. The genes that contained most VNTRs, of which PTPRN2 and DLGAP2 are the most prominent examples, were found to be predominantly expressed in the brain and associated with a wide variety of neurological disorders. Repeat-induced variation represents a sizeable fraction of the genetic variation in human genomes and should be included in investigations of genetic factors associated with phenotypic traits, specifically those associated with neurological disorders. We make available the long and short-read sequence data of the supercentenarian genome, and a compendium of SVs as identified across 5 human haplotypes.
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Affiliation(s)
- Jasper Linthorst
- grid.484519.5Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands ,grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Wim Meert
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Matthew S. Hestand
- grid.5596.f0000 0001 0668 7884Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jonas Korlach
- grid.423340.20000 0004 0640 9878Pacific Biosciences, Menlo Park, CA USA
| | | | - Marcel J. T. Reinders
- grid.5292.c0000 0001 2097 4740Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Henne Holstege
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands. .,Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands. .,Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.
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17
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Katsumata Y, Fardo DW, Bachstetter AD, Artiushin SC, Wang WX, Wei A, Brzezinski LJ, Nelson BG, Huang Q, Abner EL, Anderson S, Patel I, Shaw BC, Price DA, Niedowicz DM, Wilcock DW, Jicha GA, Neltner JH, Van Eldik LJ, Estus S, Nelson PT. Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene. J Neuropathol Exp Neurol 2020; 79:3-21. [PMID: 31748784 PMCID: PMC8204704 DOI: 10.1093/jnen/nlz116] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/18/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023] Open
Abstract
We found evidence of late-onset Alzheimer disease (LOAD)-associated genetic polymorphism within an exon of Mucin 6 (MUC6) and immediately downstream from another gene: Adaptor Related Protein Complex 2 Subunit Alpha 2 (AP2A2). PCR analyses on genomic DNA samples confirmed that the size of the MUC6 variable number tandem repeat (VNTR) region was highly polymorphic. In a cohort of autopsied subjects with quantitative digital pathology data (n = 119), the size of the polymorphic region was associated with the severity of pTau pathology in neocortex. In a separate replication cohort of autopsied subjects (n = 173), more pTau pathology was again observed in subjects with longer VNTR regions (p = 0.031). Unlike MUC6, AP2A2 is highly expressed in human brain. AP2A2 expression was lower in a subset analysis of brain samples from persons with longer versus shorter VNTR regions (p = 0.014 normalizing with AP2B1 expression). Double-label immunofluorescence studies showed that AP2A2 protein often colocalized with neurofibrillary tangles in LOAD but was not colocalized with pTau proteinopathy in progressive supranuclear palsy, or with TDP-43 proteinopathy. In summary, polymorphism in a repeat-rich region near AP2A2 was associated with neocortical pTau proteinopathy (because of the unique repeats, prior genome-wide association studies were probably unable to detect this association), and AP2A2 was often colocalized with neurofibrillary tangles in LOAD.
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Affiliation(s)
- Yuriko Katsumata
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Adam D Bachstetter
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Sergey C Artiushin
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Wang-Xia Wang
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Angela Wei
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Lena J Brzezinski
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Bela G Nelson
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Qingwei Huang
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Erin L Abner
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Sonya Anderson
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Indumati Patel
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Benjamin C Shaw
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Douglas A Price
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Dana M Niedowicz
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Donna W Wilcock
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Gregory A Jicha
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Janna H Neltner
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Linda J Van Eldik
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Steven Estus
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
| | - Peter T Nelson
- Sanders-Brown Center on Aging (YK, DWF, ADB, SCA, W-XW, AW, LJB, BGN, QH, ELA, SA, IP, DAP, DMN, DWW, GAJ, LJVE, PTN); Department of Biostatistics (YK, DWF); Spinal Cord & Brain Injury Research Center (ADB); Department of Neuroscience (ADB, DWW, LJVE); Department of Epidemiology (ELA); Department of Neurology (DWW, GAJ); Department of Physiology (BCS, SE); and Department of Pathology (W-XW, JHN, PTN), University of Kentucky, Lexington, Kentucky
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18
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Thursina C, Nurputra DK, Harahap ISK, Harahap NIF, Sa'adah N, Wibowo S, Sutarni S, Sadewa AH, Hanjaya H, Nishio H. Determining the association between polymorphisms of the DAT1 and DRD4 genes with attention deficit hyperactivity disorder in children from Java Island. Neurol Int 2020; 12:8292. [PMID: 32774820 PMCID: PMC7378541 DOI: 10.4081/ni.2020.8292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 09/09/2019] [Indexed: 12/25/2022] Open
Abstract
Attention deficit hyperactivity disorder (ADHD) is one of the most common neurobehavioural in the children. Genetic factor is known one of the factors which contributed in ADHD development. VNTR polymorphism in 3'UTR exon 15 of DAT1 gene and exon 3 of DRD4 gene are reported to be associated in ADHD. In this study we examine the association of ADHD with VNTR polymorphism of DAT1 and DRD4 gene in Indonesian children. Sixty-five ADHD children and 70 normal children (6-13 years of age), were included in the study, we matched by age and gender. ADHD was diagnosed by DSM-IV. We performed a casecontrol study to found the association between ADHD and VNTR polymorphism of DAT1 and DRD4 genes. The 10-repeat allele of DAT1 and 2-repeat allele of DRD4 were higher in Indonesian children. Although the frequency of these allele was higher, but it was similar both in ADHD and control groups. Neither DAT1 nor DRD4 gene showed showed significant difference in genotype distribution and frequency allele between both groups (p > 0.05). No association between ADHD and VNTR polymorphism of DAT1 and DRD4 genes found in Indonesian children. This data suggest that DAT1 and DRD4 do not contribute to etiology of ADHD in Indonesian children. Further studies are needed to clarify association between VNTR polymorphism of DAT1 and DRD4 genetic with ADHD of Indonesian children in larger sample size and family based study.
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Affiliation(s)
- Cempaka Thursina
- Doctoral Programme of Medical and Health Science, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Neurology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dian Kesumapramudya Nurputra
- Department of Pediatrics, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
- Department of Community Medicine and Social Health Care Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Nur Imma Fatimah Harahap
- Department of Community Medicine and Social Health Care Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Nihayatus Sa'adah
- Department of Biochemistry, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Samekto Wibowo
- Department of Neurology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sri Sutarni
- Department of Neurology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Ahmad Hamim Sadewa
- Department of Biochemistry, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hermawan Hanjaya
- Department of Neurology, Faculty of Medicine Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hisahide Nishio
- Department of Community Medicine and Social Health Care Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Pediatrics, Kobe University Graduate school of Medicine, Kobe, Japan
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19
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Nelson PT, Fardo DW, Katsumata Y. The MUC6/AP2A2 Locus and Its Relevance to Alzheimer's Disease: A Review. J Neuropathol Exp Neurol 2020; 79:568-584. [PMID: 32357373 PMCID: PMC7241941 DOI: 10.1093/jnen/nlaa024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
We recently reported evidence of Alzheimer's disease (AD)-linked genetic variation within the mucin 6 (MUC6) gene on chromosome 11p, nearby the adaptor-related protein complex 2 subunit alpha 2 (AP2A2) gene. This locus has interesting features related to human genomics and clinical research. MUC6 gene variants have been reported to potentially influence viral-including herpesvirus-immunity and the gut microbiome. Within the MUC6 gene is a unique variable number of tandem repeat (VNTR) region. We discovered an association between MUC6 VNTR repeat expansion and AD pathologic severity, particularly tau proteinopathy. Here, we review the relevant literature. The AD-linked VNTR polymorphism may also influence AP2A2 gene expression. AP2A2 encodes a polypeptide component of the adaptor protein complex, AP-2, which is involved in clathrin-coated vesicle function and was previously implicated in AD pathogenesis. To provide background information, we describe some key knowledge gaps in AD genetics research. The "missing/hidden heritability problem" of AD is highlighted. Extensive portions of the human genome, including the MUC6 VNTR, have not been thoroughly evaluated due to limitations of existing high-throughput sequencing technology. We present and discuss additional data, along with cautionary considerations, relevant to the hypothesis that MUC6 repeat expansion influences AD pathogenesis.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Pathology, University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Yuriko Katsumata
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
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20
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Bertuzzi M, Tang D, Calligaris R, Vlachouli C, Finaurini S, Sanges R, Goldwurm S, Catalan M, Antonutti L, Manganotti P, Pizzolato G, Pezzoli G, Persichetti F, Carninci P, Gustincich S. A human minisatellite hosts an alternative transcription start site for NPRL3 driving its expression in a repeat number-dependent manner. Hum Mutat 2020; 41:807-824. [PMID: 31898848 DOI: 10.1002/humu.23974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 11/16/2019] [Accepted: 12/24/2019] [Indexed: 12/21/2022]
Abstract
Minisatellites, also called variable number of tandem repeats (VNTRs), are a class of repetitive elements that may affect gene expression at multiple levels and have been correlated to disease. Their identification and role as expression quantitative trait loci (eQTL) have been limited by their absence in comparative genomic hybridization and single nucleotide polymorphisms arrays. By taking advantage of cap analysis of gene expression (CAGE), we describe a new example of a minisatellite hosting a transcription start site (TSS) which expression is dependent on the repeat number. It is located in the third intron of the gene nitrogen permease regulator like protein 3 (NPRL3). NPRL3 is a component of the GAP activity toward rags 1 protein complex that inhibits mammalian target of rapamycin complex 1 (mTORC1) activity and it is found mutated in familial focal cortical dysplasia and familial focal epilepsy. CAGE tags represent an alternative TSS identifying TAGNPRL3 messenger RNAs (mRNAs). TAGNPRL3 is expressed in red blood cells both at mRNA and protein levels, it interacts with its protein partner NPRL2 and its overexpression inhibits cell proliferation. This study provides an example of a minisatellite that is both a TSS and an eQTL as well as identifies a new VNTR that may modify mTORC1 activity.
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Affiliation(s)
| | - Dave Tang
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Raffaella Calligaris
- Area of Neuroscience, SISSA, Trieste, Italy.,Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | | | - Sara Finaurini
- Area of Neuroscience, SISSA, Trieste, Italy.,Department of Health Sciences, Università del Piemonte Orientale and IRCAD, Novara, Italy
| | - Remo Sanges
- Area of Neuroscience, SISSA, Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
| | | | - Mauro Catalan
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Lucia Antonutti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Paolo Manganotti
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Gilberto Pizzolato
- Department of Medical Sciences, Neurology Unit, University of Trieste, Trieste, Italy
| | - Gianni Pezzoli
- Parkinson Institute, ASST G. Pini-CTO, ex ICP, Milan, Italy
| | - Francesca Persichetti
- Department of Health Sciences, Università del Piemonte Orientale and IRCAD, Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan.,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Japan
| | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy.,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova, Italy
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21
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De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D’Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K. NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION. Genome Biol 2019; 20:239. [PMID: 31727106 PMCID: PMC6857246 DOI: 10.1186/s13059-019-1856-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022] Open
Abstract
Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.
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Affiliation(s)
- Arne De Roeck
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Liene Bossaerts
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Cacace
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, Center for Molecular Neurology, VIB - University of Antwerp, Antwerp, Belgium
| | - Jasper Van Dongen
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Svenn D’Hert
- Neuromics Support Facility, Center for Molecular Neurology, VIB - University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, Center for Molecular Neurology, VIB - University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, Center for Molecular Neurology, VIB - University of Antwerp, Antwerp, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group, VIB Center for Molecular Neurology, University of Antwerp-CDE, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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22
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Ilonen J, Lempainen J, Veijola R. The heterogeneous pathogenesis of type 1 diabetes mellitus. Nat Rev Endocrinol 2019; 15:635-650. [PMID: 31534209 DOI: 10.1038/s41574-019-0254-y] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Type 1 diabetes mellitus (T1DM) results from the destruction of pancreatic β-cells that is mediated by the immune system. Multiple genetic and environmental factors found in variable combinations in individual patients are involved in the development of T1DM. Genetic risk is defined by the presence of particular allele combinations, which in the major susceptibility locus (the HLA region) affect T cell recognition and tolerance to foreign and autologous molecules. Multiple other loci also regulate and affect features of specific immune responses and modify the vulnerability of β-cells to inflammatory mediators. Compared with the genetic factors, environmental factors that affect the development of T1DM are less well characterized but contact with particular microorganisms is emerging as an important factor. Certain infections might affect immune regulation, and the role of commensal microorganisms, such as the gut microbiota, are important in the education of the developing immune system. Some evidence also suggests that nutritional factors are important. Multiple islet-specific autoantibodies are found in the circulation from a few weeks to up to 20 years before the onset of clinical disease and this prediabetic phase provides a potential opportunity to manipulate the islet-specific immune response to prevent or postpone β-cell loss. The latest developments in understanding the heterogeneity of T1DM and characterization of major disease subtypes might help in the development of preventive treatments.
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Affiliation(s)
- Jorma Ilonen
- Institue of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Turku, Finland.
| | - Johanna Lempainen
- Institue of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Paediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Riitta Veijola
- Department of Paediatrics, University of Oulu and Oulu University Hospital, Oulu, Finland
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23
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Rasool SUA, Ashraf S, Nabi M, Rashid F, Masoodi SR, Fazili KM, Amin S. Insulin gene VNTR class III allele is a risk factor for insulin resistance in Kashmiri women with polycystic ovary syndrome. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100597] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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24
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Border R, Johnson EC, Evans LM, Smolen A, Berley N, Sullivan PF, Keller MC. No Support for Historical Candidate Gene or Candidate Gene-by-Interaction Hypotheses for Major Depression Across Multiple Large Samples. Am J Psychiatry 2019; 176:376-387. [PMID: 30845820 PMCID: PMC6548317 DOI: 10.1176/appi.ajp.2018.18070881] [Citation(s) in RCA: 329] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Interest in candidate gene and candidate gene-by-environment interaction hypotheses regarding major depressive disorder remains strong despite controversy surrounding the validity of previous findings. In response to this controversy, the present investigation empirically identified 18 candidate genes for depression that have been studied 10 or more times and examined evidence for their relevance to depression phenotypes. METHODS Utilizing data from large population-based and case-control samples (Ns ranging from 62,138 to 443,264 across subsamples), the authors conducted a series of preregistered analyses examining candidate gene polymorphism main effects, polymorphism-by-environment interactions, and gene-level effects across a number of operational definitions of depression (e.g., lifetime diagnosis, current severity, episode recurrence) and environmental moderators (e.g., sexual or physical abuse during childhood, socioeconomic adversity). RESULTS No clear evidence was found for any candidate gene polymorphism associations with depression phenotypes or any polymorphism-by-environment moderator effects. As a set, depression candidate genes were no more associated with depression phenotypes than noncandidate genes. The authors demonstrate that phenotypic measurement error is unlikely to account for these null findings. CONCLUSIONS The study results do not support previous depression candidate gene findings, in which large genetic effects are frequently reported in samples orders of magnitude smaller than those examined here. Instead, the results suggest that early hypotheses about depression candidate genes were incorrect and that the large number of associations reported in the depression candidate gene literature are likely to be false positives.
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Affiliation(s)
- Richard Border
- Institute for Behavioral Genetics, University of Colorado Boulder, Stockholm, Sweden,Department of Psychology and Neuroscience, University of Colorado Boulder, Stockholm, Sweden,Department of Applied Mathematics, University of Colorado Boulder, Stockholm, Sweden
| | - Emma C. Johnson
- Institute for Behavioral Genetics, University of Colorado Boulder, Stockholm, Sweden,Department of Psychiatry, Washington University School of Medicine, Stockholm, Sweden
| | - Luke M. Evans
- Institute for Behavioral Genetics, University of Colorado Boulder, Stockholm, Sweden,Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Stockholm, Sweden
| | - Andrew Smolen
- Institute for Behavioral Genetics, University of Colorado Boulder, Stockholm, Sweden
| | - Noah Berley
- Department of Psychology and Neuroscience, University of Colorado Boulder, Stockholm, Sweden
| | - Patrick F. Sullivan
- Department of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Stockholm, Sweden,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Matthew C. Keller
- Institute for Behavioral Genetics, University of Colorado Boulder, Stockholm, Sweden,Department of Psychology and Neuroscience, University of Colorado Boulder, Stockholm, Sweden
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25
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Imputation of behavioral candidate gene repeat variants in 486,551 publicly-available UK Biobank individuals. Eur J Hum Genet 2019; 27:963-969. [PMID: 30723318 DOI: 10.1038/s41431-019-0349-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 01/09/2019] [Accepted: 01/16/2019] [Indexed: 02/06/2023] Open
Abstract
Some of the most widely studied variants in psychiatric genetics include variable number tandem repeat variants (VNTRs) in SLC6A3, DRD4, SLC6A4, and MAOA. While initial findings suggested large effects, their importance with respect to psychiatric phenotypes is the subject of much debate with broadly conflicting results. Despite broad interest, these loci remain absent from the largest available samples, such as the UK Biobank, limiting researchers' ability to test these contentious hypotheses rigorously in large samples. Here, using two independent reference datasets, we report out-of-sample imputation accuracy estimates of >0.96 for all four VNTR variants and one modifying SNP, depending on the reference and target dataset. We describe the imputation procedures of these candidate variants in 486,551 UK Biobank individuals, and have made the imputed variant data available to UK Biobank researchers. This resource, provided to the scientific community, will allow the most rigorous tests to-date of the roles of these variants in behavioral and psychiatric phenotypes.
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V. Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res 2018; 28:1709-1719. [PMID: 30352806 PMCID: PMC6211647 DOI: 10.1101/gr.235119.118] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/02/2018] [Indexed: 12/20/2022]
Abstract
Whole-genome sequencing is increasingly used to identify Mendelian variants in clinical pipelines. These pipelines focus on single-nucleotide variants (SNVs) and also structural variants, while ignoring more complex repeat sequence variants. Here, we consider the problem of genotyping Variable Number Tandem Repeats (VNTRs), composed of inexact tandem duplications of short (6–100 bp) repeating units. VNTRs span 3% of the human genome, are frequently present in coding regions, and have been implicated in multiple Mendelian disorders. Although existing tools recognize VNTR carrying sequence, genotyping VNTRs (determining repeat unit count and sequence variation) from whole-genome sequencing reads remains challenging. We describe a method, adVNTR, that uses hidden Markov models to model each VNTR, count repeat units, and detect sequence variation. adVNTR models can be developed for short-read (Illumina) and single-molecule (Pacific Biosciences [PacBio]) whole-genome and whole-exome sequencing, and show good results on multiple simulated and real data sets.
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Affiliation(s)
- Mehrdad Bakhtiari
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
| | - Sharona Shleizer-Burko
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Melissa Gymrek
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA.,Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Vikas Bansal
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093, USA
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Genovese LM, Geraci F, Corrado L, Mangano E, D'Aurizio R, Bordoni R, Severgnini M, Manzini G, De Bellis G, D'Alfonso S, Pellegrini M. A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies. Front Genet 2018; 9:155. [PMID: 29770143 PMCID: PMC5941971 DOI: 10.3389/fgene.2018.00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/13/2018] [Indexed: 11/29/2022] Open
Abstract
Polymorphic Tandem Repeat (PTR) is a common form of polymorphism in the human genome. A PTR consists in a variation found in an individual (or in a population) of the number of repeating units of a Tandem Repeat (TR) locus of the genome with respect to the reference genome. Several phenotypic traits and diseases have been discovered to be strongly associated with or caused by specific PTR loci. PTR are further distinguished in two main classes: Short Tandem Repeats (STR) when the repeating unit has size up to 6 base pairs, and Variable Number Tandem Repeats (VNTR) for repeating units of size above 6 base pairs. As larger and larger populations are screened via high throughput sequencing projects, it becomes technically feasible and desirable to explore the association between PTR and a panoply of such traits and conditions. In order to facilitate these studies, we have devised a method for compiling catalogs of PTR from assembled genomes, and we have produced a catalog of PTR for genic regions (exons, introns, UTR and adjacent regions) of the human genome (GRCh38). We applied four different TR discovery software tools to uncover in the first phase 55,223,485 TR (after duplicate removal) in GRCh38, of which 373,173 were determined to be PTR in the second phase by comparison with five assembled human genomes. Of these, 263,266 are not included by state-of-the-art PTR catalogs. The new methodology is mainly based on a hierarchical and systematic application of alignment-based sequence comparisons to identify and measure the polymorphism of TR. While previous catalogs focus on the class of STR of small total size, we remove any size restrictions, aiming at the more general class of PTR, and we also target fuzzy TR by using specific detection tools. Similarly to other previous catalogs of human polymorphic loci, we focus our catalog toward applications in the discovery of disease-associated loci. Validation by cross-referencing with existing catalogs on common clinically-relevant loci shows good concordance. Overall, this proposed census of human PTR in genic regions is a shared resource (web accessible), complementary to existing catalogs, facilitating future genome-wide studies involving PTR.
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Affiliation(s)
| | - Filippo Geraci
- Institute for Informatics and Telematics of CNR, Pisa, Italy
| | - Lucia Corrado
- Department of Health Sciences, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
| | | | | | - Roberta Bordoni
- Institute for Biomedical Technologies of CNR, Segrate, Italy
| | | | - Giovanni Manzini
- Institute for Informatics and Telematics of CNR, Pisa, Italy.,Department of Science and Technological Innovation, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
| | | | - Sandra D'Alfonso
- Department of Health Sciences, University of Eastern Piedmont Amedeo Avogadro, Novara, Italy
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Say YH. The association of insertions/deletions (INDELs) and variable number tandem repeats (VNTRs) with obesity and its related traits and complications. J Physiol Anthropol 2017; 36:25. [PMID: 28615046 PMCID: PMC5471687 DOI: 10.1186/s40101-017-0142-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/01/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Despite the fact that insertions/deletions (INDELs) are the second most common type of genetic variations and variable number tandem repeats (VNTRs) represent a large portion of the human genome, they have received far less attention than single nucleotide polymorphisms (SNPs) and larger forms of structural variation like copy number variations (CNVs), especially in genome-wide association studies (GWAS) of complex diseases like polygenic obesity. This is exemplified by the vast amount of review papers on the role of SNPs and CNVs in obesity, its related traits (like anthropometric measurements, biochemical variables, and eating behavior), and its related complications (like hypertension, hypertriglyceridemia, hypercholesterolemia, and insulin resistance-collectively known as metabolic syndrome). Hence, this paper reviews the types of INDELs and VNTRs that have been studied for association with obesity and its related traits and complications. These INDELs and VNTRs could be found in the obesity loci or genes from the earliest GWAS and candidate gene association studies, like FTO, genes in the leptin-proopiomelanocortin pathway, and UCP2/3. Given the important role of the brain serotonergic and dopaminergic reward system in obesity susceptibility, the association of INDELs and VNTRs in these neurotransmitters' metabolism and transport genes with obesity is also reviewed. Next, the role of INS VNTR in obesity and its related traits is questionable, since recent large-scale studies failed to replicate the earlier positive associations. As obesity results in chronic low-grade inflammation of the adipose tissue, the proinflammatory cytokine gene IL1RA and anti-inflammatory cytokine gene IL4 have VNTRs that are implicated in obesity. A systemic proinflammatory state in combination with activation of the renin-angiotensin system and decreased nitric oxide bioavailability as found in obesity leads to endothelial dysfunction. This explains why VNTR and INDEL in eNOS and ACE, respectively, could be predisposing factors of obesity. Finally, two novel genes, DOCK5 and PER3, which are involved in the regulation of the Akt/MAPK pathway and circadian rhythm, respectively, have VNTRs and INDEL that might be associated with obesity. SHORT CONCLUSION In conclusion, INDELs and VNTRs could have important functional consequences in the pathophysiology of obesity, and research on them should be continued to facilitate obesity prediction, prevention, and treatment.
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Affiliation(s)
- Yee-How Say
- Department of Biomedical Science, Faculty of Science, Universiti Tunku Abdul Rahman (UTAR) Kampar Campus, Jalan Universiti, Bandar Barat, 31900, Kampar, Perak, Malaysia.
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Bischoff AR, Pokhvisneva I, Léger É, Gaudreau H, Steiner M, Kennedy JL, O’Donnell KJ, Diorio J, Meaney MJ, Silveira PP. Dynamic interaction between fetal adversity and a genetic score reflecting dopamine function on developmental outcomes at 36 months. PLoS One 2017; 12:e0177344. [PMID: 28505190 PMCID: PMC5432105 DOI: 10.1371/journal.pone.0177344] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
Background Fetal adversity, evidenced by poor fetal growth for instance, is associated with increased risk for several diseases later in life. Classical cut-offs to characterize small (SGA) and large for gestational age (LGA) newborns are used to define long term vulnerability. We aimed at exploring the possible dynamism of different birth weight cut-offs in defining vulnerability in developmental outcomes (through the Bayley Scales of Infant and Toddler Development), using the example of a gene vs. fetal adversity interaction considering gene choices based on functional relevance to the studied outcome. Methods 36-month-old children from an established prospective birth cohort (Maternal Adversity, Vulnerability, and Neurodevelopment) were classified according to birth weight ratio (BWR) (SGA ≤0.85, LGA >1.15, exploring a wide range of other cut-offs) and genotyped for polymorphisms associated with dopamine signaling (TaqIA-A1 allele, DRD2-141C Ins/Ins, DRD4 7-repeat, DAT1-10- repeat, Met/Met-COMT), composing a score based on the described function, in which hypofunctional variants received lower scores. Results There were 251 children (123 girls and 128 boys). Using the classic cut-offs (0.85 and 1.15), there were no statistically significant interactions between the neonatal groups and the dopamine genetic score. However, when changing the cut-offs, it is possible to see ranges of BWR that could be associated with vulnerability to poorer development according to the variation in the dopamine function. Conclusion The classic birth weight cut-offs to define SGA and LGA newborns should be seen with caution, as depending on the outcome in question, the protocols for long-term follow up could be either too inclusive—therefore most costly, or unable to screen true vulnerabilities—and therefore ineffective to establish early interventions and primary prevention.
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Affiliation(s)
- Adrianne R. Bischoff
- Department of Pediatrics, Division of Neonatology, University of Toronto and the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Irina Pokhvisneva
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
| | - Étienne Léger
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
| | - Hélène Gaudreau
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
| | - Meir Steiner
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - James L. Kennedy
- Department of Psychiatry, University of Toronto and Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Kieran J. O’Donnell
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
- Child and Brain Development Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Josie Diorio
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
| | - Michael J. Meaney
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Patrícia P. Silveira
- Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Douglas Mental Health University Institute, Montreal, Quèbec, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec, Canada
- * E-mail:
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Nikumbh S, Pfeifer N. Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. BMC Bioinformatics 2017; 18:218. [PMID: 28420341 PMCID: PMC5395875 DOI: 10.1186/s12859-017-1624-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/05/2017] [Indexed: 11/25/2022] Open
Abstract
Background Knowing the three-dimensional (3D) structure of the chromatin is important for obtaining a complete picture of the regulatory landscape. Changes in the 3D structure have been implicated in diseases. While there exist approaches that attempt to predict the long-range chromatin interactions, they focus only on interactions between specific genomic regions — the promoters and enhancers, neglecting other possibilities, for instance, the so-called structural interactions involving intervening chromatin. Results We present a method that can be trained on 5C data using the genetic sequence of the candidate loci to predict potential genome-wide interaction partners of a particular locus of interest. We have built locus-specific support vector machine (SVM)-based predictors using the oligomer distance histograms (ODH) representation. The method shows good performance with a mean test AUC (area under the receiver operating characteristic (ROC) curve) of 0.7 or higher for various regions across cell lines GM12878, K562 and HeLa-S3. In cases where any locus did not have sufficient candidate interaction partners for model training, we employed multitask learning to share knowledge between models of different loci. In this scenario, across the three cell lines, the method attained an average performance increase of 0.09 in the AUC. Performance evaluation of the models trained on 5C data regarding prediction on an independent high-resolution Hi-C dataset (which is a rather hard problem) shows 0.56 AUC, on average. Additionally, we have developed new, intuitive visualization methods that enable interpretation of sequence signals that contributed towards prediction of locus-specific interaction partners. The analysis of these sequence signals suggests a potential general role of short tandem repeat sequences in genome organization. Conclusions We demonstrated how our approach can 1) provide insights into sequence features of locus-specific interaction partners, and 2) also identify their cell-line specificity. That our models deem short tandem repeat sequences as discriminative for prediction of potential interaction partners, suggests that they could play a larger role in genome organization. Thus, our approach can (a) be beneficial to broadly understand, at the sequence-level, chromatin interactions and higher-order structures like (meta-) topologically associating domains (TADs); (b) study regions omitted from existing prediction approaches using various information sources (e.g., epigenetic information); and (c) improve methods that predict the 3D structure of the chromatin. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1624-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sarvesh Nikumbh
- Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Building E1.4, Saarbruecken, D-66123, Germany.
| | - Nico Pfeifer
- Computational Biology & Applied Algorithmics, Max Planck Institute for Informatics, Saarland Informatics Campus, Building E1.4, Saarbruecken, D-66123, Germany.,Present address: Department of Computer Science, University of Tübingen, Sand 14, Tübingen, D-72076, Germany
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Klaassen K, Stankovic B, Kotur N, Djordjevic M, Zukic B, Nikcevic G, Ugrin M, Spasovski V, Srzentic S, Pavlovic S, Stojiljkovic M. New PAH gene promoter KLF1 and 3'-region C/EBPalpha motifs influence transcription in vitro. J Appl Genet 2016; 58:79-85. [PMID: 27447460 DOI: 10.1007/s13353-016-0359-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/01/2016] [Accepted: 06/30/2016] [Indexed: 11/28/2022]
Abstract
Phenylketonuria (PKU) is a metabolic disease caused by mutations in the phenylalanine hydroxylase (PAH) gene. Although the PAH genotype remains the main determinant of PKU phenotype severity, genotype-phenotype inconsistencies have been reported. In this study, we focused on unanalysed sequences in non-coding PAH gene regions to assess their possible influence on the PKU phenotype. We transiently transfected HepG2 cells with various chloramphenicol acetyl transferase (CAT) reporter constructs which included PAH gene non-coding regions. Selected non-coding regions were indicated by in silico prediction to contain transcription factor binding sites. Furthermore, electrophoretic mobility shift assay (EMSA) and supershift assays were performed to identify which transcriptional factors were engaged in the interaction. We found novel KLF1 motif in the PAH promoter, which decreases CAT activity by 50 % in comparison to basal transcription in vitro. The cytosine at the c.-170 promoter position creates an additional binding site for the protein complex involving KLF1 transcription factor. Moreover, we assessed for the first time the role of a multivariant variable number tandem repeat (VNTR) region located in the 3'-region of the PAH gene. We found that the VNTR3, VNTR7 and VNTR8 constructs had approximately 60 % of CAT activity. The regulation is mediated by the C/EBPalpha transcription factor, present in protein complex binding to VNTR3. Our study highlighted two novel promoter KLF1 and 3'-region C/EBPalpha motifs in the PAH gene which decrease transcription in vitro and, thus, could be considered as PAH expression modifiers. New transcription motifs in non-coding regions will contribute to better understanding of the PKU phenotype complexity and may become important for the optimisation of PKU treatment.
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Affiliation(s)
- Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Biljana Stankovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Nikola Kotur
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Maja Djordjevic
- Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", School of Medicine, University of Belgrade, Radoja Dakića 6-8, 11070, Belgrade, Serbia
| | - Branka Zukic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Gordana Nikcevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Sanja Srzentic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11010, Belgrade, Serbia.
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Yang Y, Chan L. Monogenic Diabetes: What It Teaches Us on the Common Forms of Type 1 and Type 2 Diabetes. Endocr Rev 2016; 37:190-222. [PMID: 27035557 PMCID: PMC4890265 DOI: 10.1210/er.2015-1116] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
To date, more than 30 genes have been linked to monogenic diabetes. Candidate gene and genome-wide association studies have identified > 50 susceptibility loci for common type 1 diabetes (T1D) and approximately 100 susceptibility loci for type 2 diabetes (T2D). About 1-5% of all cases of diabetes result from single-gene mutations and are called monogenic diabetes. Here, we review the pathophysiological basis of the role of monogenic diabetes genes that have also been found to be associated with common T1D and/or T2D. Variants of approximately one-third of monogenic diabetes genes are associated with T2D, but not T1D. Two of the T2D-associated monogenic diabetes genes-potassium inward-rectifying channel, subfamily J, member 11 (KCNJ11), which controls glucose-stimulated insulin secretion in the β-cell; and peroxisome proliferator-activated receptor γ (PPARG), which impacts multiple tissue targets in relation to inflammation and insulin sensitivity-have been developed as major antidiabetic drug targets. Another monogenic diabetes gene, the preproinsulin gene (INS), is unique in that INS mutations can cause hyperinsulinemia, hyperproinsulinemia, neonatal diabetes mellitus, one type of maturity-onset diabetes of the young (MODY10), and autoantibody-negative T1D. Dominant heterozygous INS mutations are the second most common cause of permanent neonatal diabetes. Moreover, INS gene variants are strongly associated with common T1D (type 1a), but inconsistently with T2D. Variants of the monogenic diabetes gene Gli-similar 3 (GLIS3) are associated with both T1D and T2D. GLIS3 is a key transcription factor in insulin production and β-cell differentiation during embryonic development, which perturbation forms the basis of monogenic diabetes as well as its association with T1D. GLIS3 is also required for compensatory β-cell proliferation in adults; impairment of this function predisposes to T2D. Thus, monogenic forms of diabetes are invaluable "human models" that have contributed to our understanding of the pathophysiological basis of common T1D and T2D.
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Affiliation(s)
- Yisheng Yang
- Division of Endocrinology (Y.Y.), Department of Medicine, MetroHealth Medical Center, Case Western Reserve University, Cleveland, Ohio 44109; and Diabetes and Endocrinology Research Center (L.C.), Division of Diabetes, Endocrinology and Metabolism, Departments of Medicine, Molecular and Cellular Biology, Biochemistry and Molecular Biology, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Lawrence Chan
- Division of Endocrinology (Y.Y.), Department of Medicine, MetroHealth Medical Center, Case Western Reserve University, Cleveland, Ohio 44109; and Diabetes and Endocrinology Research Center (L.C.), Division of Diabetes, Endocrinology and Metabolism, Departments of Medicine, Molecular and Cellular Biology, Biochemistry and Molecular Biology, and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
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A novel polymorphic repeat in the upstream regulatory region of the estrogen-induced gene EIG121 is not associated with the risk of developing breast or endometrial cancer. BMC Res Notes 2016; 9:287. [PMID: 27230222 PMCID: PMC4882813 DOI: 10.1186/s13104-016-2086-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The estrogen-induced gene 121 (EIG121) has been associated with breast and endometrial cancers, but its mechanism of action remains unknown. In a genome-wide search for tandem repeats, we found that EIG121 contains a short tandem repeat (STR) in its upstream regulatory region which has the potential to alter gene expression. The presence of this STR has not previously been analysed in relation to breast or endometrial cancer risk. RESULTS In this study, the lengths of this STR were determined by PCR, fragment analysis and sequencing using DNA from 223 breast cancer patients, 204 endometrial cancer patients and 220 healthy controls to determine if they were associated with the risk of developing breast or endometrial cancer. We found this repeat to be highly variable with the number of copies of the AG motif ranging from 27 to 72 and having a bimodal distribution. No statistically significant association was identified between the length of this STR and the risk of developing breast or endometrial cancer or age at diagnosis. CONCLUSIONS The STR in the upstream regulatory region of EIG121 is highly polymorphic, but is not associated with the risk of developing breast or endometrial cancer in the cohorts analysed here. While this polymorphic STR in the regulatory region of EIG121 appears to have no impact on the risk of developing breast or endometrial cancer, its association with disease recurrence or overall survival remains to be determined.
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Cui J, Luo J, Kim YC, Snyder C, Becirovic D, Downs B, Lynch H, Wang SM. Differences of Variable Number Tandem Repeats in XRCC5 Promoter Are Associated with Increased or Decreased Risk of Breast Cancer in BRCA Gene Mutation Carriers. Front Oncol 2016; 6:92. [PMID: 27148484 PMCID: PMC4829605 DOI: 10.3389/fonc.2016.00092] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/29/2016] [Indexed: 01/04/2023] Open
Abstract
Ku80 is a subunit of the Ku heterodimer that binds to DNA double-strand break ends as part of the non-homologous end joining (NHEJ) pathway. Ku80 is also involved in homologous recombination (HR) via its interaction with BRCA1. Ku80 is encoded by the XRCC5 gene that contains a variable number tandem repeat (VNTR) insertion in its promoter region. Different VNTR genotypes can alter XRCC5 expression and affect Ku80 production, thereby affecting NHEJ and HR pathways. VNTR polymorphism is associated with multiple types of sporadic cancer. In this study, we investigated its potential association with familial breast cancer at the germline level. Using PCR, PAGE, Sanger sequencing, and statistical analyses, we compared VNTR genotypes in the XRCC5 promoter between healthy individuals and three types of familial breast cancer cases: mutated BRCA1 (BRCA1+), mutated BRCA2 (BRCA2+), and wild-type BRCA1/BRCA2 (BRCAx). We observed significant differences of VNTR genotypes between control and BRCA1+ group (P < 0.0001) and BRCA2+ group (P = 0.0042) but not BRCAx group (P = 0.2185), and the differences were significant between control and cancer-affected BRCA1+ cases (P < 0.0001) and BRCA2+ cases (P = 0.0092) but not cancer-affected BRCAx cases (P = 0.4251). Further analysis indicated that 2R/2R (OR = 1.94, 95%CI = 1.26–2.95, P = 0.0096) and 2R/1R (OR = 1.58, 95%CI = 1.11–2.26, P = 0.0388) were associated with increased risk but 1R/1R (OR = 0.55, 95%CI = 0.35–0.84, P = 0.0196) and 1R/0R (OR = 0, 95%CI = 0–0.29, P = 0.0012) were associated with decreased risk in cancer-affected BRCA1+ group; 2R/1R (OR = 1.94, 95%CI = 1.14–3.32, P = 0.0242) was associated with increased risk in cancer-affected BRCA2+ group. No correlation was observed for the altered risk between cancer-affected or -unaffected carriers and between different age of cancer diagnosis in cancer-affected carriers. The frequently observed VNTR association with in BRCA1+ and BRCA2+ breast cancer group indicates that VNTR polymorphism in the XRCC5 promoter is associated with altered risk of breast cancer in BRCA1+ and BRCA2+ carriers.
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Affiliation(s)
- Jian Cui
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center , Omaha, NE , USA
| | - Jiangtao Luo
- Department of Biostatistics, College of Public Health, University of Nebraska Medical Center , Omaha, NE , USA
| | - Yeong C Kim
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center , Omaha, NE , USA
| | - Carrie Snyder
- Department of Preventive Medicine, Hereditary Cancer Center, Creighton University , Omaha, NE , USA
| | - Dina Becirovic
- Department of Preventive Medicine, Hereditary Cancer Center, Creighton University , Omaha, NE , USA
| | - Bradley Downs
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center , Omaha, NE , USA
| | - Henry Lynch
- Department of Preventive Medicine, Hereditary Cancer Center, Creighton University , Omaha, NE , USA
| | - San Ming Wang
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center , Omaha, NE , USA
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Complete sequencing and characterization of equine aggrecan. Vet Comp Orthop Traumatol 2015; 28:79-87. [PMID: 25632964 DOI: 10.3415/vcot-14-05-0069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 09/12/2014] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To fully sequence and characterize equine aggrecan and confirm conservation of major aggrecanase, calpain and matrix metalloproteinase (MMP) cleavage sites. METHODS Reverse transcription-polymerase chain reaction and rapid amplification of cDNA ends were used to generate clones that encompassed the complete equine aggrecan sequence. Clones were sequenced and compared with the equine genome database to determine intron-exon boundaries. RESULTS The aggrecan gene spans over 61 kb on chromosome 1 and is encoded by 17 exons. Two major variants of aggrecan were cloned; one containing 8187 bp (2728 amino acids) and a second sequence of 8061 nucleotides (2686 amino acids). The variation was due to a CS1 domain polymorphism. Both sequences are substantially larger than predicted by the genomic database; 11 CS1 repeat elements are absent in the database sequence. The equine amino acid sequence was compared with human, bovine and murine sequences. Globular domains 1, 2 and 3 are highly conserved (overall identity over 80%). Equine CS1 is considerably larger than in other species and, therefore, is the least conserved domain (an overall amino acid identity of 22%). Previously defined aggrecanase, calpain and MMP cleavage sites were identified. Western blotting of chondrocyte culture samples showed complex post-secretion processing. CLINICAL SIGNIFICANCE The complete equine aggrecan sequence will support more in-depth research on aggrecan processing and degradation in equine articular cartilage and other musculoskeletal tissues.
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Sano M, Nakagawa M, Oishi A, Yasui Y, Katsube-Tanaka T. Diversification of 13S globulins, allergenic seed storage proteins, of common buckwheat. Food Chem 2014; 155:192-8. [PMID: 24594174 DOI: 10.1016/j.foodchem.2014.01.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/11/2013] [Accepted: 01/15/2014] [Indexed: 11/28/2022]
Abstract
The α polypeptide of the 13S globulin subunit of common buckwheat is the counterpart of the major allergenic β polypeptide. Trypsin digestibility varies between variants of the α polypeptide with and without a tandem repeat insert. To evaluate the intra-species diversity of 13S globulin, the comprehensive screening of a genomic DNA library was performed, resulting in the isolation of 14 and 3 genes for Met-poor and Met-rich subunits, respectively. Although most tandem repeat units were 45 bp in length, the two-repeat gene Glb2B and all one-repeat genes contained an additional 3 bp. Secondary structure predictions and polyacrylamide gel electrophoresis demonstrated that the sense strand of Glb2B-CCG, the additional 3 bp-deletion clone of Glb2B, formed a more rigid secondary structure than that of the wild-type. Thus, the large intra-species variation of 13S globulin revealed in this study and its diversification might be attributable to the unique nature of the tandem repeat sequences.
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Affiliation(s)
- Madoka Sano
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Mariko Nakagawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Akifumi Oishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
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